Alpha-amylases (alpha-1,4 glucan-4-glucanohydrolase, EC 3.2.1.1) constitute a group of enzymes which is capable of hydrolyzing starch and other linear and branched 1,4-glucosidic oligo- and polysaccharides. Almost all alpha-amylases studied have a few conserved regions with approximately the same length and spacing. One of these regions resembles the Ca2+ binding site of calmodulin and the others are thought to be necessary for the active centre and/or binding of the substrate.
While the amino acid sequence and thus primary structure of a large number of alpha-amylases are known, it has proved very difficult to determine the three-dimensional structure of all alpha-amylases. The three-dimensional structure can be determined by X-ray crystallographic analysis of alpha-amylase crystals, but it has proven difficult to obtain alpha-amylase crystals suitable for actually solving the structure.
Until now the three-dimensional structure of only a few alpha-amylases have been determined at high resolution. These include the structure of the Aspergillus oryzae TAKA alpha-amylase (Swift et al., 1991), the Aspergillus niger acid amylase (Brady et al., 1991), the structure of pig pancreatic alpha-amylase (Qian et al., 1993), and the barley alpha-amylase (Kadziola et al., 1994, J. Mol. Biol. 239: 104-121, Kadziola, thesis, Dept of Chemistry, U. of Copenhagen, Denmark). Furthermore, the three-dimensional structure of a Bacillus circulans cyclodextrin glycosyltransferase (CGTase) is known (Klein et al., 1992; Lawson et al., 1994). The CGTase catalyzes the same type of reactions as alpha-amylases and exhibits some structural resemblance with alpha-amylases.
Furthermore, crystallization and preliminary X-ray studies of B. subtilis alpha-amylases have been described (Chang et al., 1992, and Mizuno et al., 1993). No final B. subtilis structure has been reported. Analogously, the preparation of B. licheniformis alpha-amylase crystals has been reported (Suzuki et al., 1990), but no subsequent report on X-ray crystallographic analysis or three-dimensional structure is available.
Several research teams have attempted to build three-dimensional structures on the basis of the above known alpha-amylase structures. For instance, Vihinen et al. (J. Biochem. 107: 267-272 (1990)), disclose the modeling (or computer simulation) of a three-dimensional structure of the Bacillus stearothermophilus alpha-amylase on the basis of the TAKA amylase structure. The model was used to investigate hypothetical structural consequences of various site-directed mutations of the B. stearothermophilus alpha-amylase. MacGregor (1987) predicts the presence of alpha-helices and beta-barrels in alpha-amylases from different sources, including barley, pig pancreas and Bacillus amyloliquefaciens on the basis of the known structure of the A. oryzae TAKA alpha-amylase and secondary structure predicting algorithms. Furthermore, the possible loops and subsites which may be found to be present in, e.g., the B. amyloliquefaciens alpha-amylase are predicted (based on a comparison with the A. oryzae sequence and structure).
MacGregor (Starch/Stärke 45(7): 232-237 (1993)) presents a review of the relationship between the structure and activity of alpha-amylase related enzymes.
Hitherto, no three-dimensional structure has been available for the industrially important Bacillus alpha-amylases (which in the present context are termed “Termamyl-like alpha-amylases”), including the B. licheniformis, the B. amyloliquefaciens, and the B. stearothermophilus alpha-amylase.